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Research Outputs 2009 2019

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Article
2019
Open Access
File
Vertebrate Photoreceptor Cells
Oxidative Phosphorylation
Amyloid
Photoreceptor Cells
Alzheimer Disease

Comparative proteomics investigation of central carbon metabolism in Euglena gracilis grown under predominantly phototrophic, mixotrophic and heterotrophic cultivations

Hasan, M. T., Sun, A., Khatiwada, B., McQuade, L., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2019, In : Algal Research. 43, 11 p., 101638.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
proteomics
metabolism
carbon
enzymes

Evidence from the proteome for local adaptation to extreme heat in a widespread tree species

Maher, T., Mirzaei, M., Pascovici, D., Wright, I. J., Haynes, P. A. & Gallagher, R. V., Mar 2019, In : Functional Ecology. 33, 3, p. 436-446 11 p.

Research output: Contribution to journalArticleResearchpeer-review

local adaptation
proteome
heat
protein
Eucalyptus grandis
Open Access
File
proteomics
water stress
drought
rice
cultivars

Loss of Shp2 rescues BDNF/TrkB signaling and contributes to improved retinal ganglion cell neuroprotection

Chitranshi, N., Dheer, Y., Mirzaei, M., Wu, Y., Salekdeh, G. H., Abbasi, M., Gupta, V., Vander Wall, R., You, Y., Graham, S. L. & Gupta, V., 6 Feb 2019, In : Molecular Therapy. 27, 2, p. 424-441 18 p.

Research output: Contribution to journalArticleResearchpeer-review

trkB Receptor
Retinal Ganglion Cells
Glaucoma
Endoplasmic Reticulum Stress
Apoptosis

Proteomes of leaf-growing zones in rice genotypes with contrasting drought tolerance

Wu, Y., Mirzaei, M., Pascovici, D., Haynes, P. A. & Atwell, B. J., May 2019, In : Proteomics. 19, 9, 11 p., 1800310.

Research output: Contribution to journalArticleResearchpeer-review

Drought
Droughts
Proteome
Genotype
Drying

Retinoid x receptor modulation protects against ER stress response and rescues glaucoma phenotypes in adult mice

Dheer, Y., Chitranshi, N., Gupta, V., Sharma, S., Pushpitha, K., Abbasi, M., Mirzaei, M., You, Y., Graham, S. L. & Gupta, V., 1 Apr 2019, In : Experimental Neurology. 314, p. 111-125 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Retinoid X Receptors
Retinoids
Glaucoma
Phenotype
Retina

Root endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming

Ghaffari, M. R., Mirzaei, M., Ghabooli, M., Khatabi, B., Wu, Y., Zabet-Moghaddam, M., Mohammadi-Nejad, G., Haynes, P. A., Hajirezaei, M. R., Sepehri, M. & Salekdeh, G. H., 1 Jan 2019, In : Environmental and Experimental Botany. 157, p. 197-210 14 p.

Research output: Contribution to journalArticleResearchpeer-review

proteomics
drought stress
barley
water stress
fungus

The quest for missing proteins in rice

Rahiminejad, M., Ledari, M. T., Mirzaei, M., Ghorbanzadeh, Z., Kavousi, K., Ghaffari, M. R., Haynes, P. A., Komatsu, S. & Salekdeh, G. H., 7 Jan 2019, In : Molecular Plant. 12, 1, p. 4-6 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Protein Biosynthesis
Amyloid beta-Protein Precursor
Retina
Alzheimer Disease
Up-Regulation
2018

BDNF polymorphism: a review of its diagnostic and clinical relevance in neurodegenerative disorders

Shen, T., You, Y., Joseph, C., Mirzaei, M., Klistorner, A., Graham, S. L. & Gupta, V., 1 Jun 2018, In : Aging and Disease. 9, 3, p. 523-536 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Brain-Derived Neurotrophic Factor
Neurodegenerative Diseases
Valine
Methionine
Glaucoma

Bexarotene modulates Retinoid-X-receptor expression and is protective against neurotoxic endoplasmic reticulum stress response and apoptotic pathway activation

Dheer, Y., Chitranshi, N., Gupta, V., Abbasi, M., Mirzaei, M., You, Y., Chung, R., Graham, S. L. & Gupta, V., Dec 2018, In : Molecular Neurobiology. 55, 12, p. 9043-9056 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Retinoid X Receptors
Endoplasmic Reticulum Stress
Retinoid X Receptor gamma
Retinoid X Receptor beta
Brain

Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis

Emery, S. J., Baker, L., Ansell, B. R. E., Mirzaei, M., Haynes, P. A., McConville, M. J., Svärd, S. G. & Jex, A. R., 1 Apr 2018, In : GigaScience. 7, 4, p. 1-22 22 p., giy024.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Discovery of novel cell surface markers for purification of embryonic dopamine progenitors for transplantation in Parkinson's disease animal models

Fathi, A., Mirzaei, M., Dolatyar, B., Sharifitabar, M., Bayat, M., Shahbazi, E., Lee, J., Javan, M., Zhang, S-C., Gupta, V., Lee, B., Haynes, P. A., Baharvand, H. & Salekdeh, G. H., 1 Sep 2018, In : Molecular and Cellular Proteomics. 17, 9, p. 1670-1684 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Pluripotent Stem Cells
Contactin 2
Stem cells
Purification
Parkinson Disease

Distinct changes in the proteome profile of endometrial tissues in polycystic ovary syndrome compared with healthy fertile women

Amjadi, F., Mehdizadeh, M., Ashrafi, M., Nasrabadi, D., Taleahmad, S., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Aflatoonian, R., Aug 2018, In : Reproductive BioMedicine Online. 37, 2, p. 184-200 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Polycystic Ovary Syndrome
Proteome
Proteins
14-3-3 Proteins
Luteal Phase

Distribution and development of molecularly distinct perineuronal nets in visual thalamus

Sabbagh, U., Monavarfeshani, A., Su, K., Zabet-Moghadam, M., Cole, J., Carnival, E., Su, J., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Fox, M. A., Dec 2018, In : Journal of Neurochemistry. 147, 5, p. 626-646 21 p.

Research output: Contribution to journalArticleResearchpeer-review

Geniculate Bodies
Retinal Ganglion Cells
Thalamus
Retina
Rodentia

Prospective isolation of ISL1+ cardiac progenitors from human ESCs for myocardial infarction therapy

Ghazizadeh, Z., Fattahi, F., Mirzaei, M., Bayersaikhan, D., Lee, J., Chae, S., Hwang, D., Byun, K., Tabar, M. S., Taleahmad, S., Mirshahvaladi, S., Shabani, P., Fonoudi, H., Haynes, P. A., Baharvand, H., Aghdami, N., Evans, T., Lee, B. & Salekdeh, G. H., 13 Mar 2018, In : Stem Cell Reports. 10, 3, p. 848-859 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Activated-Leukocyte Cell Adhesion Molecule
Muscle
Myocardial Infarction
Stem cells
Smooth Muscle Myocytes

Retinal changes in Alzheimer's disease: disease mechanisms to evaluation perspectives

Mirzaei, M., Gupta, V. B. & Gupta, V. K., 2018, In : Journal of Neurology & Neuromedicine. 3, 2, p. 11-13 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

The Art of validating quantitative proteomics data

Handler, D. C., Pascovici, D., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Haynes, P. A., Dec 2018, In : Proteomics. 18, 23, p. 1-6 6 p., 1800222.

Research output: Contribution to journalArticleResearchpeer-review

Art
Proteomics
Western Blotting
Publications
Guidelines
2017

A comprehensive assessment of the biosynthetic pathways of ascorbate, alpha-tocopherol and free amino acids in Euglena gracilis var. saccharophila

Hasan, M. T., Sun, A., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2017, In : Algal Research. 27, p. 140-151 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
free amino acids
alpha-tocopherol
biochemical pathways
proteomics

Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes

Mirzaei, M., Gupta, V. B., Chick, J. M., Greco, T. M., Wu, Y., Chitranshi, N., Wall, R. V., Hone, E., Deng, L., Dheer, Y., Abbasi, M., Rezaeian, M., Braidy, N., You, Y., Salekdeh, G. H., Haynes, P. A., Molloy, M. P., Martins, R., Cristea, I. M., Gygi, S. P. & 2 othersGraham, S. L. & Gupta, V. K., 4 Oct 2017, In : Scientific Reports. 7, 1, p. 1-16 16 p., 12685.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Proteome
Neurodegenerative Diseases
Glaucoma
Proteins
Vitreous Body

A proteomics approach to discover drought tolerance proteins in wheat pollen grain at meiosis stage

Fotovat, R., Alikhani, M., Valizadeh, M., Mirzaei, M. & Salekdeh, G. H., 2017, In : Protein and peptide letters. 24, 1, p. 26-36 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Drought
Droughts
Meiosis
Pollen
Proteomics

Glaucoma is associated with plasmin proteolytic activation mediated through oxidative inactivation of neuroserpin

Gupta, V., Mirzaei, M., Gupta, V. B., Chitranshi, N., Dheer, Y., Vander Wall, R., Abbasi, M., You, Y., Chung, R. & Graham, S., 1 Dec 2017, In : Scientific Reports. 7, p. 1-18 18 p., 8412.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Fibrinolysin
Glaucoma
Retina
Methionine
Serpins

Low focal adhesion signaling promotes ground state pluripotency of mouse embryonic stem cells

Taleahmad, S., Mirzaei, M., Samadian, A., Hassani, S. N., Haynes, P. A., Salekdeh, G. H. & Baharvand, H., 2017, In : Journal of Proteome Research. 16, 10, p. 3585-3595 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Focal Adhesions
Stem cells
Ground state
Adhesion
Serum

PTPN11 induces endoplasmic stress and apoptosis in SH-SY5Y cells

Chitranshi, N., Dheer, Y., Gupta, V., Abbasi, M., Mirzaei, M., You, Y., Chung, R., Graham, S. L. & Gupta, V., 19 Nov 2017, In : Neuroscience. 364, p. 175-189 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Endoplasmic Reticulum Stress
Apoptosis
trkB Receptor
Up-Regulation
Dependovirus

Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia

Alikhani, M., Mirzaei, M., Sabbaghian, M., Parsamatin, P., Karamzadeh, R., Adib, S., Sodeifi, N., Gilani, M. A. S., Zabet-Moghaddam, M., Parker, L., Wu, Y., Gupta, V., Haynes, P. A., Gourabi, H., Baharvand, H. & Salekdeh, G. H., 6 Jun 2017, In : Journal of Proteomics. 162, p. 141-154 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Azoospermia
Sertoli Cell-Only Syndrome
Proteomics
Testis
Male Infertility
2016

Extended exposure to sugar and/or caffeine produces distinct behavioral and neurochemical profiles in the orbitofrontal cortex of rats: Implications for neural function

Franklin, J. L., Mirzaei, M., Wearne, T. A., Homewood, J., Goodchild, A. K., Haynes, P. A. & Cornish, J. L., 1 Nov 2016, In : Proteomics. 16, 22, p. 2894-2910 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Caffeine
Prefrontal Cortex
Sugars
Rats
Proteomics
Inflammation
Biopsy
Immune Response
muscles
Acute

Induction of virulence factors in giardia duodenalis independent of host attachment

Emery, S. J., Mirzaei, M., Vuong, D., Pascovici, D., Chick, J. M., Lacey, E. & Haynes, P. A., 12 Feb 2016, In : Scientific Reports. 6, p. 1-16 16 p., 20765.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Giardia lamblia
Trophozoites
Virulence Factors
Host-Parasite Interactions
Reactive Oxygen Species

PlantPReS: a database for plant proteome response to stress

Mousavi, S. A., Pouya, F. M., Ghaffari, M. R., Mirzaei, M., Ghaffari, A., Alikhani, M., Ghareyazie, M., Komatsu, S., Haynes, P. A. & Salekdeh, G. H., 30 Jun 2016, In : Journal of Proteomics. 143, p. 69-72 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteome
Data Mining
Databases
Heat-Shock Proteins
Proteomics
Frontal Lobe
Caffeine
Prefrontal Cortex
Proteomics
Rats
Drought
Droughts
Proteomics
Machinery
Peptide Hydrolases

Quantitative shotgun proteomics reveals extensive changes to the proteome of the orbitofrontal cortex in rats that are hyperactive following withdrawal from a high sugar diet

Franklin, J. L., Mirzaei, M., Wearne, T. A., Sauer, M. K., Homewood, J., Goodchild, A. K., Haynes, P. A. & Cornish, J. L., 1 Feb 2016, In : Proteomics. 16, 4, p. 657-673 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Firearms
Proteome
Nutrition
Prefrontal Cortex
Sugars
2015

Combining protein ratio p -values as a pragmatic approach to the analysis of multirun iTRAQ experiments

Pascovici, D., Song, X., Solomon, P. S., Winterberg, B., Mirzaei, M., Goodchild, A., Stanley, W. C., Liu, J. & Molloy, M. P., 6 Feb 2015, In : Journal of Proteome Research. 14, 2, p. 738-746 9 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteins
Experiments
Peptides
Z transforms
Statistical Models

Comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance

Faghani, E., Gharechahi, J., Komatsu, S., Mirzaei, M., Khavarinejad, R. A., Najafi, F., Farsad, L. K. & Salekdeh, G. H., 1 Jan 2015, In : Journal of Proteomics. 114, p. 1-15 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Comparative Physiology
Drought
Droughts
Physiology
Proteomics

Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress

Abdollah Hosseini, S., Gharechahi, J., Heidari, M., Koobaz, P., Abdollahi, S., Mirzaei, M., Nakhoda, B. & Hosseini Salekdeh, G., 2015, In : Functional Plant Biology. 42, 6, p. 527-542 16 p.

Research output: Contribution to journalArticleResearchpeer-review

proteomics
salt stress
salts
rice
genotype

Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance

Faghani, E., Gharechahi, J., Komatsu, S., Mirzaei, M., Ali Khavarinejad, R., Najafi, F., Karimi Farsad, L. & Hosseini Salekdeh, G., 1 Mar 2015, In : Data in Brief. 2, p. 26-28 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
physiology
drought
tolerance
induction
ontology

DDX3Y, a male-specific region of y chromosome gene, may modulate neuronal differentiation

Vakilian, H., Mirzaei, M., Sharifi Tabar, M., Pooyan, P., Habibi Rezaee, L., Parker, L., Haynes, P. A., Gourabi, H., Baharvand, H. & Salekdeh, G. H., 4 Sep 2015, In : Journal of Proteome Research. 14, 9, p. 3474-3483 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Chromosomes
Genes
Y-Linked Genes
Cells
Proteomics

Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

Percy, A. J., Tamura-Wells, J., Albar, J. P., Aloria, K., Amirkhani, A., Araujo, G. D. T., Arizmendi, J. M., Blanco, F. J., Canals, F., Cho, J. Y., Colomé-Calls, N., Corrales, F. J., Domont, G., Espadas, G., Fernandez-Puente, P., Gil, C., Haynes, P. A., Hernáez, M. L., Kim, J. Y., Kopylov, A. & 16 othersMarcilla, M., McKay, M. J., Mirzaei, M., Molloy, M. P., Ohlund, L. B., Paik, Y. K., Paradela, A., Raftery, M., Sabidó, E., Sleno, L., Wilffert, D., Wolters, J. C., Yoo, J. S., Zgoda, V., Parker, C. E. & Borchers, C. H., 1 Sep 2015, In : EuPA Open Proteomics. 8, p. 6-15 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Workflow
Quality Control
Blood Proteins
Quality control
Methamphetamine
Proteome
Prefrontal Cortex
Psychotic Disorders
Maintenance

Proteome analysis of ground state pluripotency

Taleahmad, S., Mirzaei, M., Parker, L. M., Hassani, S. N., Mollamohammadi, S., Sharifi-Zarchi, A., Haynes, P. A., Baharvand, H. & Salekdeh, G. H., 16 Dec 2015, In : Scientific Reports. 5, p. 1-10 10 p., 17985.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Proteome
Embryonic Stem Cells
Proteins
Serum
Down-Regulation
Vitis
Metabolism
Thermal stress
Sugars
Proteomics

The Hsp90 inhibitor SNX-7081 is synergistic with fludarabine nucleoside via DNA damage and repair mechanisms in human, p53-negative chronic lymphocytic leukemia

Kaufman, K. L., Jenkins, Y., Alomari, M., Mirzaei, M., Giles Best, O., Pascovici, D., Mactier, S., Mulligan, S. P., Haynes, P. A. & Christopherson, R. I., 2015, In : Oncotarget. 6, 38, p. 40981-40997 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
HSP90 Heat-Shock Proteins
B-Cell Chronic Lymphocytic Leukemia
Nucleosides
DNA Repair
DNA Damage

Two splice variants of y chromosome-located lysine-specific demethylase 5D have distinct function in prostate cancer cell line (DU-145)

Jangravi, Z., Tabar, M. S., Mirzaei, M., Parsamatin, P., Vakilian, H., Alikhani, M., Shabani, M., Haynes, P. A., Goodchild, A. K., Gourabi, H., Baharvand, H. & Salekdeh, G. H., 4 Sep 2015, In : Journal of Proteome Research. 14, 9, p. 3492-3502 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Chromosomes
Lysine
Prostatic Neoplasms
Cells
Cell Line
2014

Manipulating root water supply elicits major shifts in the shoot proteome

Mirzaei, M., Soltani, N., Sarhadi, E., George, I. S., Neilson, K. A., Pascovici, D., Shahbazian, S., Haynes, P. A., Atwell, B. J. & Salekdeh, G. H., 7 Feb 2014, In : Journal of Proteome Research. 13, 2, p. 517-526 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Water Supply
Proteome
Water supply
Droughts
Drought
2013

Proteomic analysis of the dorsal and ventral hippocampus of rats maintained on a high fat and refined sugar diet

Francis, H. M., Mirzaei, M., Pardey, M. C., Haynes, P. A. & Cornish, J. L., Oct 2013, In : Proteomics. 13, 20, p. 3076-3091 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Nutrition
Sugars
Proteomics
Rats
Hippocampus

Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley

Ghabooli, M., Khatabi, B., Ahmadi, F. S., Sepehri, M., Mirzaei, M., Amirkhani, A., Jorrín-Novo, J. V. & Salekdeh, G. H., 6 Dec 2013, In : Journal of Proteomics. 94, p. 289-301 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Drought
Hordeum
Dehydration
Proteomics
Droughts

Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed

Kottapalli, K. R., Zabet-Moghaddam, M., Rowland, D., Faircloth, W., Mirzaei, M., Haynes, P. A. & Payton, P., 1 Nov 2013, In : Journal of Proteome Research. 12, 11, p. 5048-5057 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Firearms
Proteomics
Seed
Labels
Seeds

Shotgun Proteomic Analysis of the Mexican Lime Tree Infected with "Candidatus Phytoplasma aurantifolia"

Monavarfeshani, A., Mirzaei, M., Sarhadi, E., Amirkhani, A., Khayam Nekouei, M., Haynes, P. A., Mardi, M. & Salekdeh, G. H., 1 Feb 2013, In : Journal of Proteome Research. 12, 2, p. 785-795 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Phytoplasma
Firearms
Proteomics
Infection
Proteins
2012

Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery

Mirzaei, M., Pascovici, D., Atwell, B. J. & Haynes, P. A., Mar 2012, In : Proteomics. 12, 6, p. 864-877 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Aquaporins
Monomeric GTP-Binding Proteins
Drought
Droughts
Adenosine Triphosphatases